Biology subjects

Hunter, W.

Publications and source records attributed to Hunter, W..

7 recordsLinked to original sources

bioRxiv2025

An Rhs effector uses distinct target cell functions to intoxicate bacterial and fungal competitors

Many bacteria use Type VI secretion systems (T6SSs) to deliver toxic effector proteins into neighbouring bacterial or fungal cells as a means of inter-microbial competition. Compared with numerous antibacterial effectors, few antifungal effectors have been described. Furthermore, how T6SS-delivered effectors reach their site of action in different types of target cell remains poorly understood. Here, we combine structural biology with in vivo approaches to show that Rhs2 from Serratia marcescens Db10 is a dual-kingdom T6SS-dependent DNase effector which hijacks distinct, essential target cell functions in order to reach its site of action in bacterial and fungal cells. In bacterial cells, the Rhs2 toxin domain (Rhs2CT) interacts specifically with the elongation factor, EF-Tu, and, in sibling cells, interacts with the cognate immunity protein in an unusual manner. Interaction with EF-Tu is essential for T6SS-mediated intoxication of bacterial cells by Rhs2, but not for DNase activity or intoxication of fungal cells, implying it facilitates entry of Rhs2CT across the inner membrane to the cytoplasm. Alternatively, in fungal cells, Rhs2CT translocates to the nucleus using the nuclear import machinery. Our findings reveal how a single effector domain can act against targets with distinct cellular architectures and suggest that dual-kingdom effectors may occur widely.

microbiology↗

bioRxiv2023

Computational prediction of structure, function and interaction of aphid salivary effector proteins

Similar to plant pathogens, phloem-feeding insects such as aphids deliver effector proteins inside their hosts that act to promote host susceptibility and enable feeding and infestation. Despite exciting progress towards identifying and characterizing effector proteins from these insects, their functions remain largely unknown. The recent ground-breaking development in protein structure prediction algorithms combined with the availability of proteomics and transcriptomic datasets for agriculturally important pests, such as the aphid Myzus persicae (green peach aphid), provides new opportunities to explore the structural and functional diversity of effector repertoires. In this study, we sought to gain insight into the the M. persicae effector repertoire by predicting and analysing the structures of a set of 71 effector candidate proteins. We used two protein structure prediction methods, AlphaFold and OmegaFold, which produced mutually consistent results. We observed a wide continuous spectrum of sizes and structures among the effector candidates, from disordered proteins to globular enzymes. We made use of the structural information and state-of-the-art computational methods to predict M. persicae effector protein properties, including function and interaction with host plant proteins. Overall, our investigation provides novel insights into the structure, function, and interaction prediction of aphid effector repertoires and will guide the necessary experimental characterization to address new hypotheses.

biochemistry↗

bioRxiv2021

The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm

Surfactants are used to control microbial biofilms in industrial and medical settings. Their known toxicity on aquatic biota and their longevity in the environment has encouraged research on biodegradable alternatives such as rhamnolipids. While previous research has investigated the effects of biological surfactants on single species biofilms, there remains a lack of information regarding the effects of synthetic and biological surfactants in freshwater ecosystems. We conducted a mesocosm experiment to test how the surfactant sodium dodecyl sulphate (SDS) and the biological surfactant rhamnolipid altered community composition and metabolic activity of freshwater biofilms. Biofilms were cultured in the flumes using lake water from Lake Lunz in Austria, under high (300 ppm) and low (150 ppm) concentrations of either surfactant over a four-week period. Our results show that both surfactants significantly affected microbial diversity. Up to 36% of microbial operational taxonomic units were lost after surfactant exposure. Rhamnolipid exposure also increased the production of the extracellular enzymes, leucine aminopeptidase and glucosidase, while SDS exposure reduced leucine aminopeptidase and glucosidase. This study demonstrates that exposure of freshwater biofilms to chemical and biological surfactants caused a reduction of microbial diversity and changes in biofilm metabolism, exemplified by shifts in extracellular enzyme activities. Key PointsO_LIMicrobial biofilm diversity decreased significantly after surfactant exposure. C_LIO_LIExposure to either surfactant altered extracellular enzyme activity. C_LIO_LIOverall metabolic activity was not altered, suggesting functional redundancy. C_LI

microbiology↗

bioRxiv2019

Chromosomal length reference assembly for Diaphorina citri using single-molecule sequencing and Hi-C proximity ligation with manually curated genes in developmental, structural and immune pathways

BackgroundDiaphorina citri is a vector of "Candidatus Liberibacter asiaticus" (CLas), the gram-negative bacterial pathogen associated with citrus greening disease. Control measures rely on pesticides with negative impacts on the environment, natural ecosystems and human and animal health. In contrast, gene-targeting methods have the potential to specifically target the vector species and/or reduce pathogen transmission. ResultsTo improve the genomic resources needed for targeted pest control, we assembled a D. citri genome based on PacBio long reads followed by proximity ligation-based scaffolding. The 474 Mb genome has 13 chromosomal-length scaffolds. 1,036 genes were manually curated as part of a community annotation project, composed primarily of undergraduate students. We also computationally identified a total of 1,015 putative transcription factors (TFs) and were able to infer motifs for 337 TFs (33 %). In addition, we produced a genome-independent transcriptome and genomes for D. citri endosymbionts. ConclusionsManual annotation provided more accurate gene models for use by researchers and also provided an excellent training opportunity for students from multiple institutions. All resources are available on CitrusGreening.org and NCBI. The chromosomal-length D. citri genome assembly serves as a blueprint for the development of collaborative genomics projects for other medically and agriculturally significant insect vectors.

genomics↗

bioRxiv2019

Cross-Infectivity of Vorticella across Genera of Mosquitoes for Development of Biological Mosquito Control Strategies

Protozoans in general comprise about one-third of the parasitic species infecting arthropod vectors, the role of free-living ciliates on mosquitoes have been insufficiently studied either due to their low pathogenicity or being facultative parasites. Studies have shown that exposure of Paramecium ciliate protists, like Vorticella species, to first instar Cx. nigripalpus larvae delayed larval development and reduced biomass of emerged adults due to competition for food sources like bacteria and other microbes essential to mosquito growth and survival. Thus, we report on the capacity of a Vorticella protozoans ability to cross-infect host species and parasitize multiple mosquito larvae. The unique adapted behavior with the ability to remain on the exuviae in tree hole habitats provides a novel delivery system to develop products for target species-specific mosquitocides, larvicides, or viricides to be applied and sustained in aquatic systems.

ecology↗

bioRxiv2019

17a-Estradiol limits the impact of ibuprofen upon community respiration by streambed biofilms in a sub-urban stream.

Pharmaceutical compounds such as the non-steroidal anti-inflammatory drug ibuprofen and the artificial estrogen 17-ethynylestradiol (EE2) are contaminants of emerging concern in freshwater systems. Globally, human pharmaceutical use is growing by around [~]3 % per year, yet we know little about how interactions between different pharmaceuticals may affect aquatic ecosystems. Here we test how interactions between ibuprofen and EE2 affect the growth and respiration of streambed biofilms. We used contaminant exposure experiments to quantify how these compounds affected biofilm growth (biomass), respiration, net primary production (NPP) and gross primary production (GPP), both individually and in combination. We found no effects of either ibuprofen or EE2 on biofilm biomass (using ash free dry mass as a proxy) or gross primary production. Ibuprofen significantly reduced biofilm respiration and altered NPP. Concomitant exposure to EE2, however, counteracted the inhibitory effects of ibuprofen upon biofilm respiration. Our study, thus, demonstrates that interactions between pharmaceuticals in the environment may have complex effects upon microbial contributions to aquatic ecosystem functioning.

ecology↗

bioRxiv2017

Biocuration as an undergraduate training experience: Improving the annotation of the insect vector of Citrus greening disease

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory, and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. All data are available on https://citrusgreening.org/.

genomics↗